# Makefile.am manuals:
# http://www.gnu.org/software/automake/manual/automake.html#Introduction
# http://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/

AUTOMAKE_OPTIONS = foreign

#C++ compiler command 
CXX = g++
CXXFLAGS = -Wall -fopenmp -lm -std=c++11 

# Debuging:
#CXXFLAGS = -Wall -fopenmp -lm -std=c++11 -g

# this lists the binaries to produce, the (non-PHONY, binary) targets in
# the previous manual Makefile
bin_PROGRAMS = yh-kt-fold
yh_kt_fold_SOURCES = main.cpp DotBracket.cpp KTurnMotif.cpp ReadData.cpp Settings.cpp TracebackMotif.cpp Zuker.cpp Functions/file_exists.cpp Functions/min.cpp Functions/uppercase.cpp Functions/enumerateNucleotide.cpp Functions/enumeratePairing.cpp Functions/isCanonicalPairing.cpp Motif.cpp MotifTreeElement.cpp MotifTree.cpp ScoringMatrix.cpp
